Interaction Reference Index Web Interface

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Interaction Reference Index Web Interface

metasource: Fairsharing.org
version: FAIRsharing.org: iRefWeb; Interaction Reference Index Web Interface; DOI: https://doi.org/10.25504/FAIRsharing.t31wcb; Last edited: April 26, 2021, 3:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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iRefWeb

metasource: Fairsharing.org
version: FAIRsharing.org: iRefWeb; Interaction Reference Index Web Interface; DOI: https://doi.org/10.25504/FAIRsharing.t31wcb; Last edited: April 26, 2021, 3:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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Other names: iRefWeb

iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID.

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Publications

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iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
PMID: 20940177

metasource: Fairsharing.org
version: FAIRsharing.org: iRefWeb; Interaction Reference Index Web Interface; DOI: https://doi.org/10.25504/FAIRsharing.t31wcb; Last edited: April 26, 2021, 3:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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• iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence PubMed citations: 106.

  106 articles citing: iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

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  A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661

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  IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877

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  Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. PMID:34676243

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  Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933

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  Reconstruction of Intercellular Signaling Network by Cytokine-Receptor Interactions. PMID:34179188

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  Classifying Breast Cancer Molecular Subtypes by Using Deep Clustering Approach. PMID:33324444

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  De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. PMID:33032641

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  Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567

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  MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562

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  A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372

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  GREG-studying transcriptional regulation using integrative graph databases. PMID:32055858

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  Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747

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  MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. PMID:31876329

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  MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598

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  3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients. PMID:31527881

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  Link clustering explains non-central and contextually essential genes in protein interaction networks. PMID:31406201

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  EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550

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  Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer. PMID:31221721

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  HOT or not: examining the basis of high-occupancy target regions. PMID:31114922

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  Downregulated UCHL1 Accelerates Gentamicin-Induced Auditory Cell Death via Autophagy. PMID:31041655

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  Integration of Tumor Genomic Data with Cell Lines Using Multi-dimensional Network Modules Improves Cancer Pharmacogenomics. PMID:30414925

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  IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591

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  Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization. PMID:30404858

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  Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer. PMID:30108113

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  Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644

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  An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012

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  NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. PMID:29662108

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  Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183

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  Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis. PMID:29396449

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  Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848

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  Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944

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  Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879

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  Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. PMID:27955713

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  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014

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  Computational approaches for the identification of cancer genes and pathways. PMID:27863091

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  Ten Simple Rules for Developing Public Biological Databases. PMID:27832061

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  HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551

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  G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. PMID:27546533

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  Profiling networks of distinct immune-cells in tumors. PMID:27377892

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  Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication. PMID:27373907

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  Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356

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  APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791

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  Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350

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  An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145

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  An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease. PMID:26787018

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  Evolution of disorder in Mediator complex and its functional relevance. PMID:26590257

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  Detecting modules in biological networks by edge weight clustering and entropy significance. PMID:26379697

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  Panorama of ancient metazoan macromolecular complexes. PMID:26344197

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  Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. PMID:26300911

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  Reconstruction of the temporal signaling network in Salmonella-infected human cells. PMID:26257716

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  TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708

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  Dynamics of the discovery process of protein-protein interactions from low content studies. PMID:26048415

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  FlyNet: a versatile network prioritization server for the Drosophila community. PMID:25943544

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  Unveiling Contacts within Macromolecular Assemblies by Solving Minimum Weight Connectivity Inference (MWC) Problems. PMID:25850436

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  Empowering biologists with multi-omics data: colorectal cancer as a paradigm. PMID:25527095

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  Network-based biomarkers enhance classical approaches to prognostic gene expression signatures. PMID:25521200

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  Open source libraries and frameworks for biological data visualisation: a guide for developers. PMID:25475079

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  Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies. PMID:25406591

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  Differential protein network analysis of the immune cell lineage. PMID:25309909

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  Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855

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  Bioinformatic analysis of proteomics data. PMID:25033288

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  Intercellular network structure and regulatory motifs in the human hematopoietic system. PMID:25028490

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  Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965

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  HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. PMID:24713437

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  Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. PMID:24479672

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  A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. PMID:24478706

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  Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. PMID:24448549

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  Novel protein interactions with endoglin and activin receptor-like kinase 1: potential role in vascular networks. PMID:24319055

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  A network of epigenetic regulators guides developmental haematopoiesis in vivo. PMID:24240475

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  UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987

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  Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. PMID:24162925

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  VAN: an R package for identifying biologically perturbed networks via differential variability analysis. PMID:24156242

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  Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645

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  Target essentiality and centrality characterize drug side effects. PMID:23874169

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  Digenic inheritance in medical genetics. PMID:23785127

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  The functional interactome landscape of the human histone deacetylase family. PMID:23752268

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  Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164

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  INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502

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  SH3 interactome conserves general function over specific form. PMID:23549480

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  Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PMID:23468868

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  Predicting physical interactions between protein complexes. PMID:23438732

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  A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome. PMID:23414517

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  A survey of protein interaction data and multigenic inherited disorders. PMID:23398688

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  Predicting PDZ domain mediated protein interactions from structure. PMID:23336252

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  Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes. PMID:23115478

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  Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097

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  Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. PMID:22948729

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  Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. PMID:22940862

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  Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis. PMID:22873350

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  Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. PMID:22851037

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  HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459

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  Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. PMID:22750305

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  Savant Genome Browser 2: visualization and analysis for population-scale genomics. PMID:22638571

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  Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911

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  HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130

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  Three-dimensional reconstruction of protein networks provides insight into human genetic disease. PMID:22252508

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  Evolution of biological interaction networks: from models to real data. PMID:22204388

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  The gene normalization task in BioCreative III. PMID:22151901

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  iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179

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  iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162

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  ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645

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  Interaction databases on the same page. PMID:21552234

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  Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. PMID:21447198

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  OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. PMID:21257609

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  Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497

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  SAINT: probabilistic scoring of affinity purification-mass spectrometry data. PMID:21131968

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Tags

More detailed information about this field from each metasource. ×

molecular interaction

metasource: Fairsharing.org
version: FAIRsharing.org: iRefWeb; Interaction Reference Index Web Interface; DOI: https://doi.org/10.25504/FAIRsharing.t31wcb; Last edited: April 26, 2021, 3:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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protein

metasource: Fairsharing.org
version: FAIRsharing.org: iRefWeb; Interaction Reference Index Web Interface; DOI: https://doi.org/10.25504/FAIRsharing.t31wcb; Last edited: April 26, 2021, 3:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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protein interaction

metasource: Fairsharing.org
version: FAIRsharing.org: iRefWeb; Interaction Reference Index Web Interface; DOI: https://doi.org/10.25504/FAIRsharing.t31wcb; Last edited: April 26, 2021, 3:20 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

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imex

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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ppi

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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psi-mi

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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biogrid

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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bioinformatics

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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interactions

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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macromulecules

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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protein-ligand

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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protein-protein

metasource: re3data.org
version: re3data.org: iRefWeb; editing status 2022-06-15; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31B8K last accessed: 2022-11-04

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molecular interaction protein protein interaction imex ppi psi-mi biogrid bioinformatics interactions macromulecules protein-ligand protein-protein